RESEARCH ARTICLE Notch-induced endoplasmic reticulum- associated degradation governs mouse thymocyte bÀselection Xia Liu1,2†, Jingjing Yu1,2†, Longyong Xu1,2†, Katharine Umphred-Wilson3†, Fanglue Peng1,2, Yao Ding1,2, Brendan M Barton3, Xiangdong Lv1, Michael Y Zhao1, Shengyi Sun4, Yuning Hong5, Ling Qi6, Stanley Adoro3*, Xi Chen1,2* 1Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States; 2Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, United States; 3Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, United States; 4Center for Molecular Medicine and Genetics, Wayne State University, Detroit, United States; 5Department of Chemistry and Physics, La Trobe University, Melbourne, Australia; 6Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, United States Abstract Signals from the pre-T cell receptor and Notch coordinately instruct b-selection of CD4–CD8–double negative (DN) thymocytes to generate ab T cells in the thymus. However, how these signals ensure a high-fidelity proteome and safeguard the clonal diversification of the pre- *For correspondence: selection TCR repertoire given the considerable translational activity imposed by b-selection is [email protected] (SA); largely unknown. Here, we identify the endoplasmic reticulum (ER)-associated degradation (ERAD) [email protected] (XC) machinery as a critical proteostasis checkpoint during b-selection. Expression of the SEL1L-HRD1 †These authors contributed complex, the most conserved branch of ERAD, is directly regulated by the transcriptional activity of equally to this work the Notch intracellular domain. Deletion of Sel1l impaired DN3 to DN4 thymocyte transition and ab Competing interests: The severely impaired mouse T cell development. Mechanistically, Sel1l deficiency induced authors declare that no unresolved ER stress that triggered thymocyte apoptosis through the PERK pathway. Accordingly, competing interests exist. genetically inactivating PERK rescued T cell development from Sel1l-deficient thymocytes. In contrast, IRE1a/XBP1 pathway was induced as a compensatory adaptation to alleviate Sel1l- Funding: See page 19 deficiency-induced ER stress. Dual loss of Sel1l and Xbp1 markedly exacerbated the thymic defect. Received: 03 May 2021 Our study reveals a critical developmental signal controlled proteostasis mechanism that enforces T Preprinted: 07 May 2021 cell development to ensure a healthy adaptive immunity. Accepted: 05 July 2021 Published: 09 July 2021 Reviewing editor: Juan Carlos Zu´ n˜ iga-Pflu¨ cker, University of Toronto, Sunnybrook Research Introduction Institute, Canada T cells develop from bone-marrow-derived early T-cell progenitors (ETP) through a series of well- orchestrated proliferation and differentiation steps in the thymus. In response to intrathymic interleu- Copyright Liu et al. This article kin (IL)À7 and Kit ligand, ETPs proliferate and differentiate into CD4-CD8-double negative (DN) thy- is distributed under the terms of mocytes (von Freeden-Jeffry et al., 1997). Subsequent differentiation of DN thymocytes into the Creative Commons + + - + Attribution License, which CD4 CD8 (double positive, DP) thymocytes depends on whether DN3 stage (CD44 CD25 ) thymo- permits unrestricted use and cytes successfully undergo ‘b-selection’, the first major checkpoint during ab T cell development redistribution provided that the (Shah and Zu´n˜iga-Pflu¨cker, 2014). b-selection is initiated by signals from the pre-TCR (a hetero- original author and source are dimer of the invariant pre-Ta and TCRb proteins) in DN3 thymocytes that have productively under- credited. gone V(D)J recombination at the Tcrb locus (Mallick et al., 1993; Michie and Zu´n˜iga-Pflu¨cker, Liu, Yu, Xu, et al. eLife 2021;10:e69975. DOI: https://doi.org/10.7554/eLife.69975 1 of 37 Research article Developmental Biology Immunology and Inflammation 2002). In addition to cell autonomous signal through the pre-TCR, b-selection also requires signal from the Notch receptor (Ciofani and Zu´n˜iga-Pflu¨cker, 2005; Sambandam et al., 2005). Coordi- nately, pre-TCR and Notch signals induce DN3 thymocytes to undergo 100–200 fold clonal expan- sion (Yamasaki et al., 2006; Zhao et al., 2019) as they differentiate into DN4 (CD44-CD25-) cells which give rise to the DP thymocyte precursors of mature ab T cells. This proliferative burst is crucial for the diversification of the pre-selection TCR repertoire (Kreslavsky et al., 2012) and so must be robustly buffered to ensure adequate number of thymocytes audition for positive selection. b-selec- tion imposes a considerable demand for new protein synthesis of the newly rearranged Tcrb gene and the multiple factors that execute the transcriptional and metabolic programs demanded by DN thymocyte proliferation. However, how proteome homeostasis or ‘proteostasis’ is regulated during thymocyte development is largely unknown. Endoplasmic reticulum (ER) is the major subcellular site for synthesis and maturation of all trans- membrane and secreted proteins. Protein folding is an inherently error-prone process and is tightly regulated by a myriad of chaperones and enzymes (Balchin et al., 2016; Cox et al., 2020). To main- tain proteostasis and normal cell function, cells have evolved highly sensitive and sophisticated qual- ity control systems to ensure the fidelity of protein structure, which is especially important for thymocytes undergoing b-selection that must repair protein damage and generate a functional and diverse repertoire of T cell receptors with high fidelity (Feige et al., 2015; Feige and Hendershot, 2013). Two such systems conserved across different species are ER-associated degradation (ERAD) and the unfolded protein response (UPR) (Figure 1—figure supplement 1A; Brodsky, 2012; Hwang and Qi, 2018; Walter and Ron, 2011). ERAD is the principal protein quality control mecha- nism responsible for targeting misfolded proteins in the ER for cytosolic proteasomal degradation. The E3 ubiquitin ligase HRD1 and its adaptor protein SEL1L, constitute the most conserved branch of ERAD (Brodsky, 2012; Qi et al., 2017; Ruggiano et al., 2014; Sun et al., 2014). SEL1L recruits misfolded proteins bound by ER protein chaperones to the SEL1L-HRD1 complex, through which the misfolded proteins are retrotranslocated into cytosol, ubiquitinated and degraded by the protea- some in the cytosol with the help of CDC48/ p97 (Brodsky, 2012; Nakatsukasa and Brodsky, 2008). Failure to clear the misfolded proteins in the ER activates the UPR (Brodsky, 2012; Hwang and Qi, 2018; Ruggiano et al., 2014). The UPR is a highly conserved, three-pronged path- way that is activated when the rate of cellular protein production exceeds the capacity of the ER to correctly fold and process its protein load or by various intracellular and extracellular stressors that interfere with the protein folding process. This coordinated response is mediated by three ER-local- ized transmembrane sensors: IRE1a, ATF6a, and PERK (Hetz et al., 2011). Under ER stress, IRE1a undergoes oligomerization and trans-autophosphorylation to activate its RNase domain to induce unconventional splicing of its substrate XBP1 (Hwang and Qi, 2018; Walter and Ron, 2011). ER stress also induces PERK-dependent eIF2a phosphorylation and subsequent increased cap-indepen- dent translation of ATF4 and induction of CHOP (Figure 1—figure supplement 1A; Hwang and Qi, 2018; Walter and Ron, 2011). Here, we show that ERAD is the master regulator of physiological ER proteostasis in immature DN thymocytes. The ERAD machinery was critically required for successful b-selection of DN3 thy- mocytes and consequently, ERAD deficiency impeded ab T cell development. Intriguingly, ERAD selectively preserves the cellular fitness of ab, but not gd T lymphocytes. We found that Notch sig- naling directly regulates ERAD gene expression to promote the integrity of ER proteostasis during b-selection. Activation of ERAD restricts PERK-dependent cell death in DN3 thymocytes during b- selection. Genetic inactivation of Perk rescued b-selection in Sel1l-deficient thymocytes. Results Stringent protein quality control in b-selected thymocytes To determine translational dynamics in developing thymocytes, we injected wildtype C57BL/6 (WT) mice with O-propargyl puromycin (OP-Puro), a cell-permeable puromycin analog that is incorporated into newly synthesized proteins as a measure of protein synthesis rates (Hidalgo San Jose and Signer, 2019; Tong et al., 2020). Animals were euthanized 1 hr after OP-Puro injection, and thymo- cyte subsets (gated as shown in Figure 1—figure supplement 1B,C) were assessed by flow cytome- try for OP-Puro incorporation (Figure 1A). Compared to DP and mature single positive thymocytes, Liu, Yu, Xu, et al. eLife 2021;10:e69975. DOI: https://doi.org/10.7554/eLife.69975 2 of 37 Research article Developmental Biology Immunology and Inflammation A OP-Puro TMI B C FMO * * ** *** n.s. ETP *** *** **** 20000 s. 2000 . n n.s. DN2 **** **** **** **** DN3 15000 1500 Count DN4 10000 1000 DP TMI MFI TMI SP4 5000 500 (OP-Puro MFI) (OP-Puro Protein synthesis Protein SP8 0 0 0 10 3 10 4 10 5 DP DP OP-Puro ETP DN2 DN3 DN4 SP4 SP8 ETP DN2 DN3 DN4 SP4 SP8 D Sel1l Xbp1 Hspa5 * * 0.020 ** 0.08 0.20 ** *** n.s. **** **** **** *** **** **** **** **** **** **** **** **** **** 0.015 0.06 0.15 expression 0.010 0.04 0.10 0.005 0.02 0.05 0.000 0.00 0.00 Relative mRNA expression mRNA Relative Relative mRNA Relative DP expression mRNA Relative DP DP ETP DN2 DN3 DN4 SP4 SP8 ETP DN2 DN3 DN4 SP4 SP8 ETP DN2 DN3 DN4 SP4 SP8 Dnajb9 Atf4 Ddit3 * * ** ** ** 0.025 0.04 ** 0.010 *** n.s. n.s. **** **** **** **** **** **** **** *** **** n.s. 0.020 0.03 0.008 expression expression expression 0.015 A 0.006 A A 0.02 0.010 0.004 mRN mRN mRN 0.005 0.01 0.002 ive ive 0.000 0.00 0.000 Relat Relative Relative Relative DP DP DP ETP DN2 DN3 DN4 SP4 SP8 ETP DN2 DN3 DN4 SP4 SP8 ETP DN2 DN3 DN4 SP4 SP8 Figure 1. Protein quality control in b-selected thymocytes.